layout | title | date | categories | tags |
---|---|---|---|---|
post_toc |
Amber力场相关参数文件 |
2015-11-13 14:22:55 -0800 |
CompCB |
CompBiol MD |
基于Amber14
- Amber/dat/leap/cmd/ : source加载的一系列力场等文件所在
- Amber/dat/leap/cmd/oldff : source加载的一系列力场等旧版文件所在, 如source oldff/leaprc.ff99SB
- Amber/dat/antechamber/ : antechamber处理小分子时的参数, 包括原子类型, parmchk等.
- leaprc.constph
- leaprc.ff03.r1
- leaprc.ff03ua
- leaprc.ff12SB
- leaprc.ff14ipq
- leaprc.ff14SB
- leaprc.ff14SBonlysc
- leaprc.ff14SB.redq
- leaprc.ffAM1
- leaprc.ffPM3
- leaprc.gaff
- leaprc.GLYCAM_06EPb
- leaprc.GLYCAM_06j-1
- leaprc.lipid11
- leaprc.lipid14
- leaprc.modrna08
- leaprc.parmbsc0_chiOL4_ezOL1
- leaprc.phosaa10
- leaprc.spce
- leaprc.tip3p
- leaprc.tip4pew
- oldff:
- leaprc.ff02
- leaprc.ff02polEP.r0
- leaprc.ff02polEP.r1
- leaprc.ff02pol.r0
- leaprc.ff02pol.r1
- leaprc.ff03
- leaprc.ff10
- leaprc.ff84
- leaprc.ff86
- leaprc.ff94
- leaprc.ff94.nmr
- leaprc.ff96
- leaprc.ff98
- leaprc.ff99
- leaprc.ff99bsc0
- leaprc.ff99SB
- leaprc.ff99SBildn
- leaprc.ff99SBnmr
- leaprc.GLYCAM_04
- leaprc.GLYCAM_06
- leaprc.GLYCAM_06EP
- leaprc.GLYCAM_06h
- leaprc.GLYCAM_06h-1
- leaprc.GLYCAM_06h-12SB
- leaprc.GLYCAM_06j_10
- leaprc.parmCHI_YIL.bsc
- leaprc.rna.ff02
- leaprc.rna.ff02EP
- leaprc.rna.ff84
- leaprc.rna.ff94
- leaprc.rna.ff98
- leaprc.rna.ff99
- leaprc.toyrna
- all_modrna08.frcmod
- frcmod.chcl3
- frcmod.chiOL4
- frcmod.constph
- frcmod.dc4
- frcmod.ff02pol.r1
- frcmod.ff03
- frcmod.ff03ua
- frcmod.ff12SB
- frcmod.ff14SB
- frcmod.ff99SB
- frcmod.ff99SB14
- frcmod.ff99SBildn
- frcmod.ff99SBnmr
- frcmod.ff99SP
- frcmod.ions1lsm_1264_spce
- frcmod.ions1lsm_1264_tip3p
- frcmod.ions1lsm_1264_tip4pew
- frcmod.ions1lsm_hfe_spce
- frcmod.ions1lsm_hfe_tip3p
- frcmod.ions1lsm_hfe_tip4pew
- frcmod.ions1lsm_iod
- frcmod.ions34lsm_1264_spce
- frcmod.ions34lsm_1264_tip3p
- frcmod.ions34lsm_1264_tip4pew
- frcmod.ions34lsm_hfe_spce
- frcmod.ions34lsm_hfe_tip3p
- frcmod.ions34lsm_hfe_tip4pew
- frcmod.ions34lsm_iod_spce
- frcmod.ions34lsm_iod_tip3p
- frcmod.ions34lsm_iod_tip4pew
- frcmod.ionsff99_tip3p
- frcmod.ionsjc_spce
- frcmod.ionsjc_tip3p
- frcmod.ionsjc_tip4pew
- frcmod.ionslm_1264_spce
- frcmod.ionslm_1264_tip3p
- frcmod.ionslm_1264_tip4pew
- frcmod.ionslrcm_cm_spce
- frcmod.ionslrcm_cm_tip3p
- frcmod.ionslrcm_cm_tip4pew
- frcmod.ionslrcm_hfe_spce
- frcmod.ionslrcm_hfe_tip3p
- frcmod.ionslrcm_hfe_tip4pew
- frcmod.ionslrcm_iod
- frcmod.meoh
- frcmod.nma
- frcmod.opc
- frcmod.parmbsc0
- frcmod.parmbsc0_ezOL1
- frcmod.parmCHI_YIL
- frcmod.phosaa10
- frcmod.pol3
- frcmod.protonated_nucleic
- frcmod.qspcfw
- frcmod.spce
- frcmod.spcfw
- frcmod.tip3pf
- frcmod.tip4p
- frcmod.tip4pew
- frcmod.tip5p
- frcmod.urea
- gaff.dat
- GLYCAM_06EPb.dat
- GLYCAM_06h.dat
- GLYCAM_06j.dat
- lipid11.dat
- lipid14.dat
- lj_1264_pol.dat
- nucgen.dat
- opls.info
- opls_parm.dat
- parm10.dat
- parm14ipq.dat
- parm91.dat
- parm91X.dat
- parm91X.ua.dat
- parm94.dat
- parm96.dat
- parm98.dat
- parm99.dat
- parm99EP.dat
- parmAM1.dat
- parmPM3.dat
- toyrna.dat
- all_amino03.in
- all_aminoct03.in
- all_aminont03.in
- amino10.in
- amino12.in
- aminoct10.in
- aminoct12.in
- aminont10.in
- aminont12.in
- chcl3.in
- dna_nuc94-bsc0_chiOl4-ezOL1.in
- GLYCAM_06EPb.prep
- GLYCAM_06j-1.prep
- GLYCAM_lipids_06h.prep
- meoh.in
- nma.in
- nucleic10.in
- protonated_nucleic
- toyrna.in
- uni_amino03.in
- uni_aminoct03.in
- uni_aminont03.in
- oldff
- all_amino02EP.in
- all_amino02.in
- all_amino02.r1.in
- all_amino94.in
- all_aminoct02EP.in
- all_aminoct02.in
- all_aminoct94.in
- all_aminont02EP.in
- all_aminont02.in
- all_aminont94.in
- allct.in
- all.in
- allnt.in
- all_nuc02EP.in
- all_nuc02.in
- all_nuc94.in
- GLYCAM_06h.prep
- GLYCAM_06j.prep
- na.amberua.in
- opls_nacl.in
- opls_unict.in
- opls_uni.in
- opls_unint.in
- protein.amberua.C.in
- protein.amberua.in
- protein.amberua.N.in
- unict.in
- uni.in
- unint.in
- 8Mureabox.off
- 8Murea.readme
- all_amino03.lib
- all_amino94ildn.lib
- all_amino94.lib
- all_amino94.nmr.lib
- all_aminoAM1.lib
- all_aminoct03.lib
- all_aminoct94ildn.lib
- all_aminoct94.lib
- all_aminont03.lib
- all_aminont94ildn.lib
- all_aminont94.lib
- all_aminoPM3.lib
- all_modrna08.lib
- all_nucleic94.lib
- all_nucleic94.nmr.lib
- all_prot_nucleic10.cmd
- all_prot_nucleic10.lib
- all_prot_nucleic10.log
- amino10.lib
- amino12.lib
- amino12.redq.lib
- amino14ipq.lib
- aminoct10.lib
- aminoct12.lib
- aminoct12.redq.lib
- aminoct14ip1_vac.lib
- aminoct14ipq.lib
- aminont10.lib
- aminont12.lib
- aminont12.redq.lib
- aminont14ipq.lib
- atomic_ions.cmd
- atomic_ions.lib
- atomic_ions.log
- chcl3box.off
- constph.lib
- cph_nucleic_caps.lib
- DNA_CI.lib
- ff03.cmd
- ff03.log
- ff03ua.cmd
- ff03ua.log
- ff10.cmd
- ff10.log
- ff12SB.cmd
- ff12SB.log
- ff94.cmd
- ff94.log
- GLYCAM_amino_06j_12SB.lib
- GLYCAM_aminoct_06j_12SB.lib
- GLYCAM_aminont_06j_12SB.lib
- ions94.cmd
- ions94.lib
- ions94.log
- lipid11.lib
- lipid14.lib
- lipid14_supp.lib
- Makefile
- meohbox.off
- nab10.cmd
- nab10.lib
- nab10.log
- nmabox.off
- nucleic10.lib
- nucleic12.lib
- nucleic12.redq.lib
- opcbox.off
- pol3box.off
- PTR.lib
- qspcfwbox.off
- residues.RNA.parmCHI_YIL.bsc.lib
- RNA_CI.lib
- S1P.lib
- SEP.lib
- solvents.cmd
- solvents.lib
- solvents.log
- spcebox.off
- spcfwbox.off
- T1P.lib
- tip3pbox.off
- tip3pfbox.off
- tip4pbox.off
- tip4pewbox.off
- tip5pbox.off
- TPO.lib
- uni_amino03.lib
- uni_aminoct03.lib
- uni_aminont03.lib
- Y1P.lib
- oldff
- all_amino02EP.lib
- all_amino02.lib
- all_amino02.r1.lib
- all_amino2011pol.lib
- all_amino91.lib
- all_aminoct02EP.lib
- all_aminoct02.lib
- all_aminoct2011pol.lib
- all_aminoct91.lib
- all_aminont02EP.lib
- all_aminont02.lib
- all_aminont2011pol.lib
- all_aminont91.lib
- all_nucleic02EP.lib
- all_nucleic02.lib
- all_nucleic91.lib
- dna.amberua.lib
- ff02.cmd
- ff02EP.cmd
- ff02EP.log
- ff02.log
- ff91.cmd
- ff91.log
- GLYCAM_amino_06j_10.lib
- GLYCAM_aminoct_06j_10.lib
- GLYCAM_aminont_06j_10.lib
- ions91.cmd
- ions91.lib
- pro-dna91.nmr.off
- protein.amberua.lib
- rna.amberua.lib
- APS.DAT
- ATCOR.DAT
- ATOM_EQU.TYPE
- ATOMTYPE_AMBER.DEF
- ATOMTYPE_BCC.DEF
- ATOMTYPE_CHECK.TAB
- ATOMTYPE_GAS.DEF
- ATOMTYPE_GFF.DEF
- ATOMTYPE_SYBYL.DEF
- BCCPARM.DAT
- BONDTYPE_CHECK.TAB
- CONNECT.TPL
- CORR_NAME_TYPE.DAT
- database_sample.def
- ESPPARM.DAT
- GASPARM.DAT
- mainchain_sample.dat
- PARMCHK.DAT
- RADIUS.DAT
- residuegen_sample.dat
- respgen_addfile_sample.dat
一般新版本都加载这个ff14SB力场.
leaprc.ff14SB概要
# load atom type hybridizations
addAtomTypes {...}
# Load the main parameter set.
parm10 = loadamberparams parm10.dat
frcmod14SB = loadamberparams frcmod.ff14SB
# Load main chain and terminating amino acid libraries, nucleic acids
loadOff amino12.lib
loadOff aminoct12.lib
loadOff aminont12.lib
loadOff nucleic12.lib
# Load water and ions
loadOff atomic_ions.lib
loadOff solvents.lib
HOH = TP3
WAT = TP3
# Define the PDB name map for the amino acids and nucleic acids
addPdbResMap {...}
# try to be good about reading in really old atom names as well:
addPdbAtomMap {...}
# assume that most often proteins use HIE
NHIS = NHIE
HIS = HIE
CHIS = CHIE
leaprc.ff14SB详细内容:
logFile leap.log
#
# ----- leaprc for loading the ff14SB force field
# ----- NOTE: this is designed for PDB format 3!
# Uses frcmod.ff14SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA
#
# load atom type hybridizations
#
addAtomTypes {
{ "H" "H" "sp3" }
{ "HO" "H" "sp3" }
{ "HS" "H" "sp3" }
{ "H1" "H" "sp3" }
{ "H2" "H" "sp3" }
{ "H3" "H" "sp3" }
{ "H4" "H" "sp3" }
{ "H5" "H" "sp3" }
{ "HW" "H" "sp3" }
{ "HC" "H" "sp3" }
{ "HA" "H" "sp3" }
{ "HP" "H" "sp3" }
{ "HZ" "H" "sp3" }
{ "OH" "O" "sp3" }
{ "OS" "O" "sp3" }
{ "O" "O" "sp2" }
{ "O2" "O" "sp2" }
{ "OP" "O" "sp2" }
{ "OW" "O" "sp3" }
{ "CT" "C" "sp3" }
{ "CX" "C" "sp3" }
{ "C8" "C" "sp3" }
{ "2C" "C" "sp3" }
{ "3C" "C" "sp3" }
{ "CH" "C" "sp3" }
{ "CS" "C" "sp2" }
{ "C" "C" "sp2" }
{ "CO" "C" "sp2" }
{ "C*" "C" "sp2" }
{ "CA" "C" "sp2" }
{ "CB" "C" "sp2" }
{ "CC" "C" "sp2" }
{ "CN" "C" "sp2" }
{ "CM" "C" "sp2" }
{ "CK" "C" "sp2" }
{ "CQ" "C" "sp2" }
{ "CD" "C" "sp2" }
{ "C5" "C" "sp2" }
{ "C4" "C" "sp2" }
{ "CP" "C" "sp2" }
{ "CI" "C" "sp3" }
{ "CJ" "C" "sp2" }
{ "CW" "C" "sp2" }
{ "CV" "C" "sp2" }
{ "CR" "C" "sp2" }
{ "CA" "C" "sp2" }
{ "CY" "C" "sp2" }
{ "C0" "Ca" "sp3" }
{ "MG" "Mg" "sp3" }
{ "N" "N" "sp2" }
{ "NA" "N" "sp2" }
{ "N2" "N" "sp2" }
{ "N*" "N" "sp2" }
{ "NP" "N" "sp2" }
{ "NQ" "N" "sp2" }
{ "NB" "N" "sp2" }
{ "NC" "N" "sp2" }
{ "NT" "N" "sp3" }
{ "NY" "N" "sp2" }
{ "N3" "N" "sp3" }
{ "S" "S" "sp3" }
{ "SH" "S" "sp3" }
{ "P" "P" "sp3" }
{ "LP" "" "sp3" }
{ "EP" "" "sp3" }
{ "F" "F" "sp3" }
{ "Cl" "Cl" "sp3" }
{ "Br" "Br" "sp3" }
{ "I" "I" "sp3" }
{ "F-" "F" "sp3" }
{ "Cl-" "Cl" "sp3" }
{ "Br-" "Br" "sp3" }
{ "I-" "I" "sp3" }
{ "Li+" "Li" "sp3" }
{ "Na+" "Na" "sp3" }
{ "K+" "K" "sp3" }
{ "Rb+" "Rb" "sp3" }
{ "Cs+" "Cs" "sp3" }
{ "Mg+" "Mg" "sp3" }
# glycam
{ "OG" "O" "sp3" }
{ "OL" "O" "sp3" }
{ "AC" "C" "sp3" }
{ "EC" "C" "sp3" }
}
#
# Load the main parameter set.
#
parm10 = loadamberparams parm10.dat
frcmod14SB = loadamberparams frcmod.ff14SB
#
# Load main chain and terminating amino acid libraries, nucleic acids
#
loadOff amino12.lib
loadOff aminoct12.lib
loadOff aminont12.lib
loadOff nucleic12.lib
#
# Load water and ions
#
loadOff atomic_ions.lib
loadOff solvents.lib
HOH = TP3
WAT = TP3
#
# Define the PDB name map for the amino acids and nucleic acids
#
addPdbResMap {
{ 0 "HYP" "NHYP" } { 1 "HYP" "CHYP" }
{ 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
{ 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
{ 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
{ 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
{ 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
{ 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
{ 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
{ 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
{ 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
{ 0 "HID" "NHID" } { 1 "HID" "CHID" }
{ 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
{ 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
{ 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
{ 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
{ 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
{ 0 "MET" "NMET" } { 1 "MET" "CMET" }
{ 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
{ 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
{ 0 "SER" "NSER" } { 1 "SER" "CSER" }
{ 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
{ 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
{ 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
{ 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
{ 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
{ 0 "G" "G5" } { 1 "G" "G3" }
{ 0 "A" "A5" } { 1 "A" "A3" }
{ 0 "C" "C5" } { 1 "C" "C3" }
{ 0 "U" "U5" } { 1 "U" "U3" }
{ 0 "DG" "DG5" } { 1 "DG" "DG3" }
{ 0 "DA" "DA5" } { 1 "DA" "DA3" }
{ 0 "DC" "DC5" } { 1 "DC" "DC3" }
{ 0 "DT" "DT5" } { 1 "DT" "DT3" }
# some old Amber residue names for RNA:
{ 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" }
{ 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" }
{ 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" }
{ 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" }
# some really old Amber residue names, assuming DNA:
{ 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" }
{ 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" }
{ 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" }
{ 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" }
# uncomment out the following if you have this old style RNA files:
# { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" }
# { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" }
# { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" }
# { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" }
}
# try to be good about reading in really old atom names as well:
addPdbAtomMap {
{ "O5*" "O5'" }
{ "C5*" "C5'" }
{ "C4*" "C4'" }
{ "O4*" "O4'" }
{ "C3*" "C3'" }
{ "O3*" "O3'" }
{ "C2*" "C2'" }
{ "O2*" "O2'" }
{ "C1*" "C1'" }
{ "C5M" "C7" }
{ "H1*" "H1'" }
{ "H2*1" "H2'" }
{ "H2*2" "H2''" }
{ "H2'1" "H2'" }
{ "H2'2" "H2''" }
{ "H3*" "H3'" }
{ "H4*" "H4'" }
{ "H5*1" "H5'" }
{ "H5*2" "H5''" }
{ "H5'1" "H5'" }
{ "H5'2" "H5''" }
{ "HO'2" "HO2'" }
{ "H5T" "HO5'" }
{ "H3T" "HO3'" }
{ "O1'" "O4'" }
{ "OA" "OP1" }
{ "OB" "OP2" }
{ "O1P" "OP1" }
{ "O2P" "OP2" }
}
#
# assume that most often proteins use HIE
#
NHIS = NHIE
HIS = HIE
CHIS = CHIE
leaprc.ff99SB 概要
# load atom type hybridizations
addAtomTypes {...}
# Load the main parameter set.
parm99 = loadamberparams parm99.dat
frcmod99SB = loadamberparams frcmod.ff99SB
# Load DNA/RNA libraries
loadOff all_nucleic94.lib
# Load main chain and terminating
# amino acid libraries (i.e. ff94 libs)
loadOff all_amino94.lib
loadOff all_aminoct94.lib
loadOff all_aminont94.lib
# Load water and ions
loadOff ions94.lib
loadOff solvents.lib
HOH = TP3
WAT = TP3
# Define the PDB name map for the amino acids and nucleic acids
addPdbResMap {...}
# try to be good about reading in really old atom names as well:
addPdbAtomMap {...}
# assume that most often proteins use HIE
NHIS = NHIE
HIS = HIE
CHIS = CHIE
leaprc.ff99SB 详细内容
logFile leap.log
#
# ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field
# ----- this file is updated for PDB format 3
#
# load atom type hybridizations
#
addAtomTypes {
{ "H" "H" "sp3" }
{ "HO" "H" "sp3" }
{ "HS" "H" "sp3" }
{ "H1" "H" "sp3" }
{ "H2" "H" "sp3" }
{ "H3" "H" "sp3" }
{ "H4" "H" "sp3" }
{ "H5" "H" "sp3" }
{ "HW" "H" "sp3" }
{ "HC" "H" "sp3" }
{ "HA" "H" "sp3" }
{ "HP" "H" "sp3" }
{ "OH" "O" "sp3" }
{ "OS" "O" "sp3" }
{ "O" "O" "sp2" }
{ "O2" "O" "sp2" }
{ "OW" "O" "sp3" }
{ "CT" "C" "sp3" }
{ "CH" "C" "sp3" }
{ "C2" "C" "sp3" }
{ "C3" "C" "sp3" }
{ "C" "C" "sp2" }
{ "C*" "C" "sp2" }
{ "CA" "C" "sp2" }
{ "CB" "C" "sp2" }
{ "CC" "C" "sp2" }
{ "CN" "C" "sp2" }
{ "CM" "C" "sp2" }
{ "CK" "C" "sp2" }
{ "CQ" "C" "sp2" }
{ "CD" "C" "sp2" }
{ "CE" "C" "sp2" }
{ "CF" "C" "sp2" }
{ "CP" "C" "sp2" }
{ "CI" "C" "sp2" }
{ "CJ" "C" "sp2" }
{ "CW" "C" "sp2" }
{ "CV" "C" "sp2" }
{ "CR" "C" "sp2" }
{ "CA" "C" "sp2" }
{ "CY" "C" "sp2" }
{ "C0" "Ca" "sp2" }
{ "MG" "Mg" "sp3" }
{ "N" "N" "sp2" }
{ "NA" "N" "sp2" }
{ "N2" "N" "sp2" }
{ "N*" "N" "sp2" }
{ "NP" "N" "sp2" }
{ "NQ" "N" "sp2" }
{ "NB" "N" "sp2" }
{ "NC" "N" "sp2" }
{ "NT" "N" "sp3" }
{ "N3" "N" "sp3" }
{ "S" "S" "sp3" }
{ "SH" "S" "sp3" }
{ "P" "P" "sp3" }
{ "LP" "" "sp3" }
{ "F" "F" "sp3" }
{ "CL" "Cl" "sp3" }
{ "BR" "Br" "sp3" }
{ "I" "I" "sp3" }
{ "FE" "Fe" "sp3" }
{ "EP" "" "sp3" }
# glycam
{ "OG" "O" "sp3" }
{ "OL" "O" "sp3" }
{ "AC" "C" "sp3" }
{ "EC" "C" "sp3" }
}
#
# Load the main parameter set.
#
parm99 = loadamberparams parm99.dat
frcmod99SB = loadamberparams frcmod.ff99SB
#
# Load DNA/RNA libraries
#
loadOff all_nucleic94.lib
#
# Load main chain and terminating
# amino acid libraries (i.e. ff94 libs)
#
loadOff all_amino94.lib
loadOff all_aminoct94.lib
loadOff all_aminont94.lib
#
# Load water and ions
#
loadOff ions94.lib
loadOff solvents.lib
HOH = TP3
WAT = TP3
#
# Define the PDB name map for the amino acids and DNA.
#
addPdbResMap {
{ 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
{ 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
{ 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
{ 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
{ 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
{ 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
{ 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
{ 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
{ 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
{ 0 "HID" "NHID" } { 1 "HID" "CHID" }
{ 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
{ 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
{ 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
{ 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
{ 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
{ 0 "MET" "NMET" } { 1 "MET" "CMET" }
{ 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
{ 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
{ 0 "SER" "NSER" } { 1 "SER" "CSER" }
{ 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
{ 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
{ 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
{ 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
{ 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
{ 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" }
{ 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" }
{ 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" }
{ 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" }
{ 0 "G" "RG5" } { 1 "G" "RG3" } { "G" "RG" } { "GN" "RGN" }
{ 0 "A" "RA5" } { 1 "A" "RA3" } { "A" "RA" } { "AN" "RAN" }
{ 0 "C" "RC5" } { 1 "C" "RC3" } { "C" "RC" } { "CN" "RCN" }
{ 0 "U" "RU5" } { 1 "U" "RU3" } { "U" "RU" } { "UN" "RUN" }
{ 0 "DG" "DG5" } { 1 "DG" "DG3" }
{ 0 "DA" "DA5" } { 1 "DA" "DA3" }
{ 0 "DC" "DC5" } { 1 "DC" "DC3" }
{ 0 "DT" "DT5" } { 1 "DT" "DT3" }
}
addPdbAtomMap {
{ "O5*" "O5'" }
{ "C5*" "C5'" }
{ "C4*" "C4'" }
{ "O4*" "O4'" }
{ "C3*" "C3'" }
{ "O3*" "O3'" }
{ "C2*" "C2'" }
{ "C1*" "C1'" }
{ "C5M" "C7" }
{ "O2*" "O2'" }
{ "H1*" "H1'" }
{ "H2*1" "H2'1" }
{ "H2*2" "H2'2" }
{ "H2'" "H2'1" }
{ "H2''" "H2'2" }
{ "H3*" "H3'" }
{ "H4*" "H4'" }
{ "H5*1" "H5'1" }
{ "H5*2" "H5'2" }
{ "H5'" "H5'1" }
{ "H5''" "H5'2" }
{ "HO2'" "HO'2" }
{ "HO5'" "H5T" }
{ "HO3'" "H3T" }
{ "O1'" "O4'" }
{ "OA" "O1P" }
{ "OB" "O2P" }
{ "OP1" "O1P" }
{ "OP2" "O2P" }
}
#
# assumed that most often proteins use HIE
#
NHIS = NHIE
HIS = HIE
CHIS = CHIE
leaprc.gaff 详细内容
logFile leap.log
#
# ----- leaprc for loading the general Amber Force field.
# This file is mostly for use with Antechamber
#
# load atom type hybridizations
#
addAtomTypes {
{ "h1" "H" "sp3" }
{ "h2" "H" "sp3" }
{ "h3" "H" "sp3" }
{ "h4" "H" "sp3" }
{ "h5" "H" "sp3" }
{ "ha" "H" "sp3" }
{ "hc" "H" "sp3" }
{ "hn" "H" "sp3" }
{ "ho" "H" "sp3" }
{ "hp" "H" "sp3" }
{ "hs" "H" "sp3" }
{ "hw" "H" "sp3" }
{ "hx" "H" "sp3" }
{ "o" "O" "sp2" }
{ "o2" "O" "sp2" }
{ "oh" "O" "sp3" }
{ "os" "O" "sp3" }
{ "ow" "O" "sp3" }
{ "c" "C" "sp2" }
{ "c1" "C" "sp2" }
{ "c2" "C" "sp2" }
{ "c3" "C" "sp3" }
{ "ca" "C" "sp2" }
{ "cc" "C" "sp2" }
{ "cd" "C" "sp2" }
{ "ce" "C" "sp2" }
{ "cf" "C" "sp2" }
{ "cg" "C" "sp2" }
{ "ch" "C" "sp2" }
{ "cp" "C" "sp2" }
{ "cq" "C" "sp2" }
{ "cu" "C" "sp2" }
{ "cv" "C" "sp2" }
{ "cx" "C" "sp2" }
{ "cy" "C" "sp2" }
{ "cz" "C" "sp2" }
{ "n" "N" "sp2" }
{ "n1" "N" "sp2" }
{ "n2" "N" "sp2" }
{ "n3" "N" "sp3" }
{ "n4" "N" "sp3" }
{ "na" "N" "sp2" }
{ "nb" "N" "sp2" }
{ "nc" "N" "sp2" }
{ "nd" "N" "sp2" }
{ "ne" "N" "sp2" }
{ "nf" "N" "sp2" }
{ "nh" "N" "sp2" }
{ "no" "N" "sp2" }
{ "s" "S" "sp2" }
{ "s2" "S" "sp2" }
{ "s3" "S" "sp3" }
{ "s4" "S" "sp3" }
{ "s6" "S" "sp3" }
{ "sh" "S" "sp3" }
{ "ss" "S" "sp3" }
{ "sx" "S" "sp3" }
{ "sy" "S" "sp3" }
{ "p2" "P" "sp2" }
{ "p3" "P" "sp3" }
{ "p4" "P" "sp3" }
{ "p5" "P" "sp3" }
{ "pb" "P" "sp3" }
{ "pc" "P" "sp3" }
{ "pd" "P" "sp3" }
{ "pe" "P" "sp3" }
{ "pf" "P" "sp3" }
{ "px" "P" "sp3" }
{ "py" "P" "sp3" }
{ "f" "F" "sp3" }
{ "cl" "Cl" "sp3" }
{ "br" "Br" "sp3" }
{ "i" "I" "sp3" }
}
#
# Load the general force field parameter set.
#
gaff = loadamberparams gaff.dat